while I could tell you how to fix this, it's necessary to have a very close look at the install log first. Since this instance preference is missing, who knows what's broken or missing in other places. Even though it's a production machine, maybe you should consider re-installing 4.2, or at least file a service request. The necessary steps to fix this instance will leave you with an unsupported production instance, otherwise.
this means that several other instance preferences are also missing. There must have been install errors, although the install log you provided did not show any. Maybe it was from a different install.
Sorry, I can not post instructions how to fix this by directly modifying the Apex repository. Apart from missing instance preferences, other parts could be broken, too. The safest option is to export all workspaces and re-install Apex.
Thanks. I agree with you. It is not safe to run this instance now.
I will be thankful if you can just give me some tip to minimize the workspace export/import effort. I have an idea that I will export all workspaces and application using APEXExport.class through command line. But I am worried about other objects e.g. images/staticfiles/Saved interactive reports, Interactive report subscription etc. Do you have an idea to save all of them through command line?
Just for your info, values missing from my instance are: